Jehad Serwan Mostafa, 37, a former San Diego resident, was indicted on similar charges in 2009.
Without providing specifics, the new counts accuse him of having key roles in al-Shabaab activities and providing material support from 2008 to 2017.
The FBI said it learned this year that he is a leader in al-Shabaab’s “explosives department.”
“Today, Mostafa is believed to be the highest-ranking United States citizen fighting overseas for a terrorist organization,” said Scott Brunner, the agent in charge of the FBI office in San Diego.
The group claimed responsibility for two Sept. 30 attacks on U.S. and European military targets in Somalia, including one by an estimated 25 fighters who were killed when they tried to storm the Belidogle military airstrip, which hosts Somali and U.S. forces.
Mostafa was born in Waukesha, Wisc., and raised in San Diego, where authorities say he has relatives. He graduated from the University of California, San Diego, in 2005 and — according to an FBI poster offering a $5 million reward for information leading to his arrest — joined al-Shabaab around 2006, authorities said.
Mostafa was among a handful of young Muslims from the U.S. who took high-visibility roles inside the al-Qaida-linked insurgent force, authorities said.
He was once president of the now-defunct Muslim Youth Council of San Diego, which said on its website that it was “dedicated to showing the world that Islam is a religion of peace and Muslims are a peaceful and productive part of society.”
Mostafa’s father, Halim Mostafa, a Kurdish Syrian, made a low-budget film, “Mozlym,” that was released in 2008 and billed as an effort to show how the true meaning of Islam is often lost amid misconceptions of non-Muslims in America.
The Associated Press contributed to this report.